Defense Primer: President’s Constitutional Authority with Regard to the Armed Forces

"Article II, Section 2, Clause 1
The President shall be Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States; he may require the Opinion, in writing, of the principal Officer in each of the executive Departments, upon any Subject relating to the Duties of their respective Office, and he shall have Power to grant Reprieves and Pardons for Offences against the United States, except in Cases of Impeachment.

Commander in Chief:
The Constitution makes the President Commander in Chief of the Armed Forces, but does not define exactly what powers he may exercise in that role. Nor does it explain the extent to which Congress, using its own constitutional powers, may influence how the President commands the Armed Forces. Separation-of-powers debates seem to arise with some frequency regarding the exercise of military powers..."
Presidential authority and armed forces